I have been having issues with this also. I have tried setting home from both flight plan and flight data screens, the home position moves, but when i write to pixhawk it does not update.
If you then read from the Pixhawk the home location bounces back to startup/boot position.
Simply dragging home position does not seem to work as well.
I did manage to move it once, but have no idea what combo of read/write and screen made it work. I have not been able to replicate it since.
I would defiantly say that setting a different home location in mission planner does not preform as expected. I am using latest rover in boat frame.